PROTOCOL FOR WIDE-GENOME SEQUENCING AND GENOTYPING OF RABIES VIRUS ISOLATES

rabies; PCR; sequencing; phylogenetic tree; strain; isolate; genotype.

Abstract

The purpose of this work is to describe a protocol for whole genome sequencing of clinical samples of Rabies lyssavirus RNA on the Illumina MiSeq platform. Previously, genotyping of the rabies virus circulating in Kazakhstan was based on the nucleoprotein gene sequence (N gene). This paper describes a method for sequencing and genotyping whole genome sequences of local rabies virus isolates. The protocol describes the methods of sample preparation, sequencing and genotyping currently used for epidemiological analysis not only of Rabies lyssavirus, but also for other viral pathogens such as SARS-CoV-2, Influenza and others. As a result, consensus sequences of the genomes of five Rabies lyssavirus isolates selected in the Atyrau region were obtained. Phylogenetic analysis was carried out and genotypes were assigned. All isolates belong to the clade Cosmopolitan CA1. The studied isolates form a single cluster with phylogenetically close isolates from Western Russia: Nizhny Novgorod region, Voronezh region, Lipetsk region, Vladimir region, Samara region.